[2023-06-29 01:04:18,190] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:04:18,193] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:04:18,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg2faa2826-6903-40d0-ba24-c3dbbf6852c1/dqc_reference
[2023-06-29 01:04:19,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:04:19,477] [INFO] Task started: Prodigal
[2023-06-29 01:04:19,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg06beeb7f-0828-4c9e-9eb8-b77c545d1edd/GCA_012965375.1_ASM1296537v1_genomic.fna.gz | prodigal -d GCA_012965375.1_ASM1296537v1_genomic.fna/cds.fna -a GCA_012965375.1_ASM1296537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:04:25,182] [INFO] Task succeeded: Prodigal
[2023-06-29 01:04:25,182] [INFO] Task started: HMMsearch
[2023-06-29 01:04:25,182] [INFO] Running command: hmmsearch --tblout GCA_012965375.1_ASM1296537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2faa2826-6903-40d0-ba24-c3dbbf6852c1/dqc_reference/reference_markers.hmm GCA_012965375.1_ASM1296537v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:04:25,431] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:04:25,432] [INFO] Found 6/6 markers.
[2023-06-29 01:04:25,463] [INFO] Query marker FASTA was written to GCA_012965375.1_ASM1296537v1_genomic.fna/markers.fasta
[2023-06-29 01:04:25,464] [INFO] Task started: Blastn
[2023-06-29 01:04:25,464] [INFO] Running command: blastn -query GCA_012965375.1_ASM1296537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2faa2826-6903-40d0-ba24-c3dbbf6852c1/dqc_reference/reference_markers.fasta -out GCA_012965375.1_ASM1296537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:04:26,049] [INFO] Task succeeded: Blastn
[2023-06-29 01:04:26,052] [INFO] Selected 9 target genomes.
[2023-06-29 01:04:26,052] [INFO] Target genome list was writen to GCA_012965375.1_ASM1296537v1_genomic.fna/target_genomes.txt
[2023-06-29 01:04:26,054] [INFO] Task started: fastANI
[2023-06-29 01:04:26,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg06beeb7f-0828-4c9e-9eb8-b77c545d1edd/GCA_012965375.1_ASM1296537v1_genomic.fna.gz --refList GCA_012965375.1_ASM1296537v1_genomic.fna/target_genomes.txt --output GCA_012965375.1_ASM1296537v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:04:32,166] [INFO] Task succeeded: fastANI
[2023-06-29 01:04:32,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2faa2826-6903-40d0-ba24-c3dbbf6852c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:04:32,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2faa2826-6903-40d0-ba24-c3dbbf6852c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:04:32,168] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:04:32,168] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 01:04:32,168] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-29 01:04:32,170] [INFO] DFAST Taxonomy check result was written to GCA_012965375.1_ASM1296537v1_genomic.fna/tc_result.tsv
[2023-06-29 01:04:32,171] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:04:32,171] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:04:32,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2faa2826-6903-40d0-ba24-c3dbbf6852c1/dqc_reference/checkm_data
[2023-06-29 01:04:32,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:04:32,208] [INFO] Task started: CheckM
[2023-06-29 01:04:32,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012965375.1_ASM1296537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012965375.1_ASM1296537v1_genomic.fna/checkm_input GCA_012965375.1_ASM1296537v1_genomic.fna/checkm_result
[2023-06-29 01:04:56,748] [INFO] Task succeeded: CheckM
[2023-06-29 01:04:56,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 01:04:56,777] [INFO] ===== Completeness check finished =====
[2023-06-29 01:04:56,778] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:04:56,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012965375.1_ASM1296537v1_genomic.fna/markers.fasta)
[2023-06-29 01:04:56,778] [INFO] Task started: Blastn
[2023-06-29 01:04:56,779] [INFO] Running command: blastn -query GCA_012965375.1_ASM1296537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2faa2826-6903-40d0-ba24-c3dbbf6852c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_012965375.1_ASM1296537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:04:57,564] [INFO] Task succeeded: Blastn
[2023-06-29 01:04:57,568] [INFO] Selected 8 target genomes.
[2023-06-29 01:04:57,569] [INFO] Target genome list was writen to GCA_012965375.1_ASM1296537v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:04:57,595] [INFO] Task started: fastANI
[2023-06-29 01:04:57,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg06beeb7f-0828-4c9e-9eb8-b77c545d1edd/GCA_012965375.1_ASM1296537v1_genomic.fna.gz --refList GCA_012965375.1_ASM1296537v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012965375.1_ASM1296537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:05:02,368] [INFO] Task succeeded: fastANI
[2023-06-29 01:05:02,377] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 01:05:02,377] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_012964265.1	s__Arctic96AD-7 sp012964265	99.0106	458	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.25	98.98	0.81	0.73	8	conclusive
GCA_016764995.1	s__Arctic96AD-7 sp016764995	83.612	494	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645085.1	s__Arctic96AD-7 sp018645085	80.5073	436	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002082305.1	s__Arctic96AD-7 sp002082305	80.5032	403	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.68	95.22	0.86	0.64	13	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	80.1544	418	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.44	95.94	0.78	0.68	5	-
GCA_014381795.1	s__Arctic96AD-7 sp014381795	79.6439	296	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182865.1	s__Arctic96AD-7 sp905182865	79.1597	394	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.26	97.17	0.94	0.88	7	-
GCA_004213175.1	s__Arctic96AD-7 sp002704555	78.1461	248	650	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.39	96.63	0.73	0.69	4	-
--------------------------------------------------------------------------------
[2023-06-29 01:05:02,379] [INFO] GTDB search result was written to GCA_012965375.1_ASM1296537v1_genomic.fna/result_gtdb.tsv
[2023-06-29 01:05:02,380] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:05:02,382] [INFO] DFAST_QC result json was written to GCA_012965375.1_ASM1296537v1_genomic.fna/dqc_result.json
[2023-06-29 01:05:02,383] [INFO] DFAST_QC completed!
[2023-06-29 01:05:02,383] [INFO] Total running time: 0h0m44s